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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9E00

Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome

Functional Information from GO Data
ChainGOidnamespacecontents
A0000786cellular_componentnucleosome
A0005515molecular_functionprotein binding
A0005576cellular_componentextracellular region
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005694cellular_componentchromosome
A0006325biological_processchromatin organization
A0006334biological_processnucleosome assembly
A0030527molecular_functionstructural constituent of chromatin
A0031492molecular_functionnucleosomal DNA binding
A0031507biological_processheterochromatin formation
A0070062cellular_componentextracellular exosome
B0000781cellular_componentchromosome, telomeric region
B0000786cellular_componentnucleosome
B0003677molecular_functionDNA binding
B0003723molecular_functionRNA binding
B0005515molecular_functionprotein binding
B0005576cellular_componentextracellular region
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005694cellular_componentchromosome
B0006325biological_processchromatin organization
B0006334biological_processnucleosome assembly
B0016020cellular_componentmembrane
B0030527molecular_functionstructural constituent of chromatin
B0032200biological_processtelomere organization
B0032991cellular_componentprotein-containing complex
B0043505cellular_componentCENP-A containing nucleosome
B0045653biological_processnegative regulation of megakaryocyte differentiation
B0061644biological_processprotein localization to CENP-A containing chromatin
B0070062cellular_componentextracellular exosome
E0000786cellular_componentnucleosome
E0005515molecular_functionprotein binding
E0005576cellular_componentextracellular region
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
E0005694cellular_componentchromosome
E0006325biological_processchromatin organization
E0006334biological_processnucleosome assembly
E0030527molecular_functionstructural constituent of chromatin
E0031492molecular_functionnucleosomal DNA binding
E0031507biological_processheterochromatin formation
E0070062cellular_componentextracellular exosome
F0000781cellular_componentchromosome, telomeric region
F0000786cellular_componentnucleosome
F0003677molecular_functionDNA binding
F0003723molecular_functionRNA binding
F0005515molecular_functionprotein binding
F0005576cellular_componentextracellular region
F0005634cellular_componentnucleus
F0005654cellular_componentnucleoplasm
F0005694cellular_componentchromosome
F0006325biological_processchromatin organization
F0006334biological_processnucleosome assembly
F0016020cellular_componentmembrane
F0030527molecular_functionstructural constituent of chromatin
F0032200biological_processtelomere organization
F0032991cellular_componentprotein-containing complex
F0043505cellular_componentCENP-A containing nucleosome
F0045653biological_processnegative regulation of megakaryocyte differentiation
F0061644biological_processprotein localization to CENP-A containing chromatin
F0070062cellular_componentextracellular exosome
M0000786cellular_componentnucleosome
M0005515molecular_functionprotein binding
M0005576cellular_componentextracellular region
M0005634cellular_componentnucleus
M0005654cellular_componentnucleoplasm
M0005694cellular_componentchromosome
M0006325biological_processchromatin organization
M0006334biological_processnucleosome assembly
M0030527molecular_functionstructural constituent of chromatin
M0031492molecular_functionnucleosomal DNA binding
M0031507biological_processheterochromatin formation
M0070062cellular_componentextracellular exosome
N0000781cellular_componentchromosome, telomeric region
N0000786cellular_componentnucleosome
N0003677molecular_functionDNA binding
N0003723molecular_functionRNA binding
N0005515molecular_functionprotein binding
N0005576cellular_componentextracellular region
N0005634cellular_componentnucleus
N0005654cellular_componentnucleoplasm
N0005694cellular_componentchromosome
N0006325biological_processchromatin organization
N0006334biological_processnucleosome assembly
N0016020cellular_componentmembrane
N0030527molecular_functionstructural constituent of chromatin
N0032200biological_processtelomere organization
N0032991cellular_componentprotein-containing complex
N0043505cellular_componentCENP-A containing nucleosome
N0045653biological_processnegative regulation of megakaryocyte differentiation
N0061644biological_processprotein localization to CENP-A containing chromatin
N0070062cellular_componentextracellular exosome
Q0000786cellular_componentnucleosome
Q0005515molecular_functionprotein binding
Q0005576cellular_componentextracellular region
Q0005634cellular_componentnucleus
Q0005654cellular_componentnucleoplasm
Q0005694cellular_componentchromosome
Q0006325biological_processchromatin organization
Q0006334biological_processnucleosome assembly
Q0030527molecular_functionstructural constituent of chromatin
Q0031492molecular_functionnucleosomal DNA binding
Q0031507biological_processheterochromatin formation
Q0070062cellular_componentextracellular exosome
R0000781cellular_componentchromosome, telomeric region
R0000786cellular_componentnucleosome
R0003677molecular_functionDNA binding
R0003723molecular_functionRNA binding
R0005515molecular_functionprotein binding
R0005576cellular_componentextracellular region
R0005634cellular_componentnucleus
R0005654cellular_componentnucleoplasm
R0005694cellular_componentchromosome
R0006325biological_processchromatin organization
R0006334biological_processnucleosome assembly
R0016020cellular_componentmembrane
R0030527molecular_functionstructural constituent of chromatin
R0032200biological_processtelomere organization
R0032991cellular_componentprotein-containing complex
R0043505cellular_componentCENP-A containing nucleosome
R0045653biological_processnegative regulation of megakaryocyte differentiation
R0061644biological_processprotein localization to CENP-A containing chromatin
R0070062cellular_componentextracellular exosome
Functional Information from PROSITE/UniProt
site_idPS00046
Number of Residues7
DetailsHISTONE_H2A Histone H2A signature. AGLqFPV
ChainResidueDetails
CALA21-VAL27
site_idPS00047
Number of Residues5
DetailsHISTONE_H4 Histone H4 signature. GAKRH
ChainResidueDetails
BGLY14-HIS18
site_idPS00094
Number of Residues13
DetailsC5_MTASE_1 C-5 cytosine-specific DNA methylases active site. DlVigGsPCnDLS
ChainResidueDetails
UASP702-SER714
VASP623-SER635
site_idPS00322
Number of Residues7
DetailsHISTONE_H3_1 Histone H3 signature 1. KAPRKQL
ChainResidueDetails
ALYS14-LEU20
site_idPS00357
Number of Residues23
DetailsHISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
ChainResidueDetails
DARG89-GLY111
site_idPS00959
Number of Residues9
DetailsHISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
ChainResidueDetails
APRO66-ILE74
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"19783980","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues16
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"20850016","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues4
DetailsModified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"29211711","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"20850016","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues4
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues4
DetailsModified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"PubMed","id":"31542297","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27436229","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues4
DetailsLipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"PubMed","id":"21076176","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues1
DetailsModified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16627869","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues1
DetailsModified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P68431","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues4
DetailsModified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"PubMed","id":"17267393","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"PubMed","id":"21724829","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17081983","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"15592455","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues4
DetailsModified residue: {"description":"N6-methacryllysine; alternate","evidences":[{"source":"PubMed","id":"34961760","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues4
DetailsModified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62806","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues4
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P62806","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI20
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"PubMed","id":"30886146","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI22
Number of Residues8
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"19818714","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI23
Number of Residues8
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI24
Number of Residues396
DetailsDomain: {"description":"ADD","evidences":[{"source":"PROSITE-ProRule","id":"PRU00865","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI25
Number of Residues90
DetailsZinc finger: {"description":"GATA-type; atypical","evidences":[{"source":"PROSITE-ProRule","id":"PRU00865","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI26
Number of Residues168
DetailsZinc finger: {"description":"PHD-type; atypical","evidences":[{"source":"PROSITE-ProRule","id":"PRU00865","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI27
Number of Residues184
DetailsRegion: {"description":"Interaction with the PRC2/EED-EZH2 complex","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI28
Number of Residues7
DetailsActive site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01016","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10018","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI29
Number of Residues32
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"Q9Y6K1","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI30
Number of Residues8
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI31
Number of Residues36
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"17713477","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2QRV","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI32
Number of Residues4
DetailsModified residue: {"description":"S-methylcysteine; by autocatalysis","evidences":[{"source":"UniProtKB","id":"O88508","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI33
Number of Residues92
DetailsRegion: {"description":"Interaction with the PRC2/EED-EZH2 complex","evidences":[{"source":"UniProtKB","id":"O88508","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

254587

PDB entries from 2026-06-03

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